Starting phenix.real_space_refine on Tue Feb 13 09:30:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2024/7upx_26677.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2024/7upx_26677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2024/7upx_26677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2024/7upx_26677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2024/7upx_26677.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upx_26677/02_2024/7upx_26677.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3112 2.51 5 N 821 2.21 5 O 977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 28": "OD1" <-> "OD2" Residue "L ASP 31": "OD1" <-> "OD2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L ASP 167": "OD1" <-> "OD2" Residue "L ASP 170": "OD1" <-> "OD2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4930 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1569 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.33, per 1000 atoms: 0.68 Number of scatterers: 4930 At special positions: 0 Unit cell: (96.28, 82.17, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 977 8.00 N 821 7.00 C 3112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 941.8 milliseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 12.1% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.072A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.579A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.232A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 191 removed outlier: 3.990A pdb=" N GLY H 190 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.652A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 188' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.513A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.877A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.524A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.205A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.317A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.411A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 154 188 hydrogen bonds defined for protein. 456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 819 1.30 - 1.43: 1420 1.43 - 1.56: 2788 1.56 - 1.69: 1 1.69 - 1.82: 23 Bond restraints: 5051 Sorted by residual: bond pdb=" C TYR H 145 " pdb=" O TYR H 145 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.22e-02 6.72e+03 2.49e+01 bond pdb=" C1 FUC B 3 " pdb=" O5 FUC B 3 " ideal model delta sigma weight residual 1.400 1.481 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" CA ARG A 466 " pdb=" C ARG A 466 " ideal model delta sigma weight residual 1.520 1.566 -0.046 1.20e-02 6.94e+03 1.45e+01 bond pdb=" C6 NAG B 1 " pdb=" O6 NAG B 1 " ideal model delta sigma weight residual 1.408 1.478 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 5046 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.87: 235 106.87 - 114.09: 2569 114.09 - 121.31: 2629 121.31 - 128.52: 1415 128.52 - 135.74: 30 Bond angle restraints: 6878 Sorted by residual: angle pdb=" C GLU H 148 " pdb=" N PRO H 149 " pdb=" CA PRO H 149 " ideal model delta sigma weight residual 119.84 133.01 -13.17 1.25e+00 6.40e-01 1.11e+02 angle pdb=" N PHE H 146 " pdb=" CA PHE H 146 " pdb=" C PHE H 146 " ideal model delta sigma weight residual 109.81 123.29 -13.48 2.21e+00 2.05e-01 3.72e+01 angle pdb=" CA PHE H 100G" pdb=" CB PHE H 100G" pdb=" CG PHE H 100G" ideal model delta sigma weight residual 113.80 119.88 -6.08 1.00e+00 1.00e+00 3.70e+01 angle pdb=" C ARG H 82B" pdb=" N LEU H 82C" pdb=" CA LEU H 82C" ideal model delta sigma weight residual 121.05 129.71 -8.66 1.43e+00 4.89e-01 3.67e+01 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.00e+00 1.00e+00 3.45e+01 ... (remaining 6873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.86: 2868 22.86 - 45.72: 119 45.72 - 68.57: 20 68.57 - 91.43: 12 91.43 - 114.29: 2 Dihedral angle restraints: 3021 sinusoidal: 1182 harmonic: 1839 Sorted by residual: dihedral pdb=" C TYR A 495 " pdb=" N TYR A 495 " pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " ideal model delta harmonic sigma weight residual -122.60 -108.66 -13.94 0 2.50e+00 1.60e-01 3.11e+01 dihedral pdb=" N TYR L 140 " pdb=" C TYR L 140 " pdb=" CA TYR L 140 " pdb=" CB TYR L 140 " ideal model delta harmonic sigma weight residual 122.80 135.52 -12.72 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" CA TYR H 91 " pdb=" C TYR H 91 " pdb=" N CYS H 92 " pdb=" CA CYS H 92 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 3018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 595 0.120 - 0.239: 147 0.239 - 0.358: 22 0.358 - 0.477: 4 0.477 - 0.596: 1 Chirality restraints: 769 Sorted by residual: chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.22e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.89e+01 chirality pdb=" CA TYR L 140 " pdb=" N TYR L 140 " pdb=" C TYR L 140 " pdb=" CB TYR L 140 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 ... (remaining 766 not shown) Planarity restraints: 886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " -0.100 2.00e-02 2.50e+03 5.75e-02 6.62e+01 pdb=" CG TYR L 32 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 90 " -0.075 2.00e-02 2.50e+03 4.78e-02 4.58e+01 pdb=" CG TYR H 90 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR H 90 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR H 90 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR H 90 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR H 90 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR H 90 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR H 90 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 91 " 0.093 2.00e-02 2.50e+03 4.74e-02 4.50e+01 pdb=" CG TYR L 91 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR L 91 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR L 91 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR L 91 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR L 91 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR L 91 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR L 91 " 0.034 2.00e-02 2.50e+03 ... (remaining 883 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 118 2.72 - 3.27: 4640 3.27 - 3.81: 7348 3.81 - 4.36: 10325 4.36 - 4.90: 16877 Nonbonded interactions: 39308 Sorted by model distance: nonbonded pdb=" OE2 GLU L 105 " pdb=" OH TYR L 140 " model vdw 2.176 2.440 nonbonded pdb=" CB GLU H 148 " pdb=" CD PRO H 149 " model vdw 2.190 3.840 nonbonded pdb=" OD1 ASP A 442 " pdb=" OG SER H 100B" model vdw 2.297 2.440 nonbonded pdb=" O ARG L 142 " pdb=" N ALA L 144 " model vdw 2.421 2.520 nonbonded pdb=" NZ LYS H 209 " pdb=" OE1 GLU L 123 " model vdw 2.429 2.520 ... (remaining 39303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 22.690 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.900 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.081 5051 Z= 0.820 Angle : 1.877 13.479 6878 Z= 1.230 Chirality : 0.106 0.596 769 Planarity : 0.012 0.120 885 Dihedral : 14.710 114.291 1837 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 1.43 % Allowed : 5.41 % Favored : 93.16 % Rotamer: Outliers : 2.20 % Allowed : 4.77 % Favored : 93.03 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.32), residues: 629 helix: -3.80 (0.43), residues: 46 sheet: 0.50 (0.33), residues: 235 loop : -0.57 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.016 TRP L 35 HIS 0.010 0.004 HIS L 198 PHE 0.063 0.014 PHE H 100G TYR 0.100 0.016 TYR L 32 ARG 0.007 0.001 ARG H 100A *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.570 Fit side-chains REVERT: A 443 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8639 (p) REVERT: H 148 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5282 (tt0) REVERT: L 48 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8753 (mp) REVERT: L 103 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8838 (mtpp) REVERT: L 188 LYS cc_start: 0.8860 (ptmm) cc_final: 0.8533 (pttm) outliers start: 12 outliers final: 5 residues processed: 109 average time/residue: 0.2301 time to fit residues: 30.2519 Evaluate side-chains 82 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN L 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5051 Z= 0.270 Angle : 0.728 10.238 6878 Z= 0.375 Chirality : 0.049 0.178 769 Planarity : 0.005 0.038 885 Dihedral : 10.362 91.464 762 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.34 % Favored : 96.18 % Rotamer: Outliers : 1.83 % Allowed : 10.09 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.34), residues: 629 helix: -2.85 (0.57), residues: 47 sheet: 0.80 (0.32), residues: 265 loop : -0.20 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 50 HIS 0.005 0.002 HIS H 35 PHE 0.034 0.002 PHE H 146 TYR 0.022 0.002 TYR L 91 ARG 0.005 0.001 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.500 Fit side-chains REVERT: A 440 ASN cc_start: 0.8461 (p0) cc_final: 0.8080 (t0) REVERT: A 443 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8826 (p) REVERT: L 167 ASP cc_start: 0.7894 (t0) cc_final: 0.7479 (t0) REVERT: L 183 LYS cc_start: 0.8297 (tptm) cc_final: 0.7822 (tptp) outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.2358 time to fit residues: 28.6963 Evaluate side-chains 79 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.0060 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5051 Z= 0.230 Angle : 0.669 9.604 6878 Z= 0.335 Chirality : 0.047 0.178 769 Planarity : 0.004 0.032 885 Dihedral : 8.072 73.529 753 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.93 % Favored : 94.75 % Rotamer: Outliers : 2.57 % Allowed : 11.38 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.34), residues: 629 helix: -2.30 (0.66), residues: 46 sheet: 0.87 (0.33), residues: 259 loop : -0.11 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 50 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.002 PHE H 146 TYR 0.022 0.002 TYR L 91 ARG 0.003 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.564 Fit side-chains REVERT: A 440 ASN cc_start: 0.8438 (p0) cc_final: 0.8113 (t0) REVERT: H 148 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5999 (tp30) REVERT: L 167 ASP cc_start: 0.7965 (t0) cc_final: 0.7493 (t0) REVERT: L 170 ASP cc_start: 0.8774 (p0) cc_final: 0.8472 (p0) REVERT: L 183 LYS cc_start: 0.8304 (tptm) cc_final: 0.7845 (tptp) outliers start: 14 outliers final: 9 residues processed: 90 average time/residue: 0.2363 time to fit residues: 26.0970 Evaluate side-chains 83 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 49 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5051 Z= 0.227 Angle : 0.637 7.889 6878 Z= 0.316 Chirality : 0.045 0.171 769 Planarity : 0.004 0.030 885 Dihedral : 6.922 58.294 751 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.13 % Favored : 95.55 % Rotamer: Outliers : 2.39 % Allowed : 12.29 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.34), residues: 629 helix: -1.45 (0.76), residues: 40 sheet: 0.87 (0.32), residues: 260 loop : -0.12 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 50 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE H 146 TYR 0.020 0.002 TYR L 91 ARG 0.002 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.548 Fit side-chains REVERT: A 440 ASN cc_start: 0.8346 (p0) cc_final: 0.8121 (t0) REVERT: A 466 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.7551 (ptp90) REVERT: L 167 ASP cc_start: 0.7950 (t0) cc_final: 0.7467 (t0) REVERT: L 183 LYS cc_start: 0.8292 (tptm) cc_final: 0.7743 (tptp) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.2210 time to fit residues: 22.2756 Evaluate side-chains 76 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5051 Z= 0.316 Angle : 0.675 8.087 6878 Z= 0.330 Chirality : 0.047 0.150 769 Planarity : 0.004 0.031 885 Dihedral : 6.405 47.998 751 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.61 % Favored : 95.07 % Rotamer: Outliers : 3.12 % Allowed : 12.66 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.34), residues: 629 helix: -1.13 (0.81), residues: 40 sheet: 0.90 (0.33), residues: 260 loop : -0.14 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.006 0.002 HIS H 35 PHE 0.015 0.002 PHE L 71 TYR 0.022 0.002 TYR L 91 ARG 0.002 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.520 Fit side-chains REVERT: A 440 ASN cc_start: 0.8429 (p0) cc_final: 0.8139 (t0) REVERT: A 466 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8050 (ptp90) REVERT: L 167 ASP cc_start: 0.7888 (t0) cc_final: 0.7358 (m-30) REVERT: L 183 LYS cc_start: 0.8366 (tptm) cc_final: 0.7789 (tptp) REVERT: L 199 GLN cc_start: 0.8556 (tt0) cc_final: 0.8123 (mt0) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.2280 time to fit residues: 23.1393 Evaluate side-chains 77 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5051 Z= 0.290 Angle : 0.649 7.334 6878 Z= 0.319 Chirality : 0.046 0.147 769 Planarity : 0.004 0.031 885 Dihedral : 5.996 40.019 749 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.29 % Favored : 95.39 % Rotamer: Outliers : 2.94 % Allowed : 14.50 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.35), residues: 629 helix: -1.14 (0.81), residues: 40 sheet: 0.91 (0.33), residues: 260 loop : -0.17 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.002 PHE H 166 TYR 0.020 0.002 TYR L 91 ARG 0.003 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.575 Fit side-chains REVERT: A 440 ASN cc_start: 0.8463 (p0) cc_final: 0.8137 (t0) REVERT: A 466 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8142 (ptp90) REVERT: H 148 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6338 (tp30) REVERT: L 167 ASP cc_start: 0.7982 (t0) cc_final: 0.7383 (m-30) REVERT: L 183 LYS cc_start: 0.8382 (tptm) cc_final: 0.7794 (tptp) REVERT: L 199 GLN cc_start: 0.8520 (tt0) cc_final: 0.8130 (mt0) outliers start: 16 outliers final: 12 residues processed: 79 average time/residue: 0.2434 time to fit residues: 23.5164 Evaluate side-chains 78 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5051 Z= 0.236 Angle : 0.620 6.917 6878 Z= 0.304 Chirality : 0.045 0.150 769 Planarity : 0.004 0.031 885 Dihedral : 5.658 33.508 749 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 2.39 % Allowed : 15.05 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.35), residues: 629 helix: -1.01 (0.82), residues: 40 sheet: 1.06 (0.33), residues: 255 loop : -0.22 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE H 166 TYR 0.019 0.002 TYR L 91 ARG 0.003 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.545 Fit side-chains REVERT: A 440 ASN cc_start: 0.8506 (p0) cc_final: 0.8126 (t0) REVERT: A 466 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8164 (ptp90) REVERT: H 117 LYS cc_start: 0.8181 (tttt) cc_final: 0.7749 (tttp) REVERT: H 148 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6381 (tp30) REVERT: L 29 ILE cc_start: 0.8654 (mm) cc_final: 0.8421 (mm) REVERT: L 167 ASP cc_start: 0.8002 (t0) cc_final: 0.7399 (m-30) REVERT: L 183 LYS cc_start: 0.8326 (tptm) cc_final: 0.7790 (tptp) REVERT: L 199 GLN cc_start: 0.8513 (tt0) cc_final: 0.8208 (mt0) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.2328 time to fit residues: 21.2978 Evaluate side-chains 75 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 33 optimal weight: 9.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5051 Z= 0.224 Angle : 0.611 6.783 6878 Z= 0.299 Chirality : 0.044 0.146 769 Planarity : 0.004 0.030 885 Dihedral : 5.503 30.026 749 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.03 % Rotamer: Outliers : 2.75 % Allowed : 15.23 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.35), residues: 629 helix: -0.98 (0.82), residues: 40 sheet: 1.09 (0.33), residues: 255 loop : -0.21 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE H 166 TYR 0.019 0.002 TYR L 91 ARG 0.003 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.578 Fit side-chains REVERT: A 440 ASN cc_start: 0.8525 (p0) cc_final: 0.8111 (t0) REVERT: A 466 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8175 (ptp90) REVERT: H 117 LYS cc_start: 0.8191 (tttt) cc_final: 0.7742 (tttp) REVERT: H 148 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6458 (tp30) REVERT: L 29 ILE cc_start: 0.8637 (mm) cc_final: 0.8432 (mm) REVERT: L 167 ASP cc_start: 0.8004 (t0) cc_final: 0.7391 (m-30) REVERT: L 183 LYS cc_start: 0.8332 (tptm) cc_final: 0.7798 (tptp) REVERT: L 199 GLN cc_start: 0.8497 (tt0) cc_final: 0.8207 (mt0) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.2467 time to fit residues: 23.9154 Evaluate side-chains 82 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5051 Z= 0.271 Angle : 0.637 6.969 6878 Z= 0.311 Chirality : 0.045 0.141 769 Planarity : 0.004 0.031 885 Dihedral : 5.625 31.686 749 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 2.57 % Allowed : 15.23 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.35), residues: 629 helix: -1.02 (0.82), residues: 40 sheet: 1.04 (0.33), residues: 255 loop : -0.29 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE L 71 TYR 0.026 0.002 TYR H 99 ARG 0.002 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.558 Fit side-chains REVERT: A 438 SER cc_start: 0.9296 (m) cc_final: 0.8932 (p) REVERT: A 440 ASN cc_start: 0.8567 (p0) cc_final: 0.8131 (t0) REVERT: A 466 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8214 (ptp90) REVERT: H 117 LYS cc_start: 0.8197 (tttt) cc_final: 0.7749 (tttp) REVERT: H 148 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6508 (tp30) REVERT: L 29 ILE cc_start: 0.8615 (mm) cc_final: 0.8401 (mm) REVERT: L 167 ASP cc_start: 0.7996 (t0) cc_final: 0.7373 (m-30) REVERT: L 183 LYS cc_start: 0.8313 (tptm) cc_final: 0.7803 (tptp) REVERT: L 199 GLN cc_start: 0.8517 (tt0) cc_final: 0.8202 (mt0) outliers start: 14 outliers final: 12 residues processed: 79 average time/residue: 0.2322 time to fit residues: 22.4564 Evaluate side-chains 80 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5051 Z= 0.259 Angle : 0.633 6.826 6878 Z= 0.309 Chirality : 0.045 0.142 769 Planarity : 0.004 0.030 885 Dihedral : 5.630 31.981 749 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.97 % Favored : 95.87 % Rotamer: Outliers : 2.75 % Allowed : 15.41 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.34), residues: 629 helix: -1.00 (0.82), residues: 40 sheet: 1.01 (0.33), residues: 255 loop : -0.30 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE L 71 TYR 0.029 0.002 TYR H 99 ARG 0.002 0.000 ARG H 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.576 Fit side-chains REVERT: A 438 SER cc_start: 0.9285 (m) cc_final: 0.8928 (p) REVERT: A 440 ASN cc_start: 0.8580 (p0) cc_final: 0.8123 (t0) REVERT: A 466 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8212 (ptp90) REVERT: H 117 LYS cc_start: 0.8183 (tttt) cc_final: 0.7736 (tttp) REVERT: H 148 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6504 (tp30) REVERT: L 29 ILE cc_start: 0.8608 (mm) cc_final: 0.8390 (mm) REVERT: L 183 LYS cc_start: 0.8308 (tptm) cc_final: 0.7798 (tptp) REVERT: L 199 GLN cc_start: 0.8505 (tt0) cc_final: 0.8196 (mt0) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.2308 time to fit residues: 22.5667 Evaluate side-chains 82 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105629 restraints weight = 6306.631| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.42 r_work: 0.3070 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5051 Z= 0.254 Angle : 0.629 6.719 6878 Z= 0.306 Chirality : 0.045 0.141 769 Planarity : 0.004 0.030 885 Dihedral : 5.617 31.156 749 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.45 % Favored : 95.39 % Rotamer: Outliers : 2.94 % Allowed : 15.23 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.34), residues: 629 helix: -0.99 (0.82), residues: 40 sheet: 0.98 (0.33), residues: 255 loop : -0.31 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE L 71 TYR 0.029 0.002 TYR H 99 ARG 0.002 0.000 ARG H 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.53 seconds wall clock time: 33 minutes 31.18 seconds (2011.18 seconds total)